Can you please tell me how to create the transform file to include the encryption key? Should I just add a row and use the Property of "encryption key" with a value of "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX" ?

Also can you write out the batch file that will check for an installed instance and then ignore installation if present?

It would seem we just need to add the new parameters to the Transform. I have not tested this using a .mst as shown in the steps above, but adding the following values the same way as you added the ENDPOINTSERVER as shown above, I think it may work. Here are the Properties that I know of that you can try adding via Orca: